Resolwe

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Added
-----
- Add support for ``Python 3.13``
- Save test folder data using actions/upload-artifact
- Allow staff users to create and update ``Variant``, ``VariantCall`` and
``VariantExperiment`` objects via API endpoint

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Django 5.1 and bump version of other
dependencies
- **BACKWARD INCOMPATIBLE:** Require Resolwe 43.x
- Use ``pyproject.toml`` instead of ``setup.py``
- Calculate up to 5 principal components in ``pca`` process
- Add ``annotation`` as nested field to ``Variant`` serializer
- Add an output field in ``alignment-star``
indicating whether input reads were downsampled
- Change the metric reporting gene body coverage in MultiQC
to align with QoRTs vignette recommendations
- Add downsampled alignment as an input to MultiQC process
in ``workflow-bbduk-star-featurecounts-qc`` workflow

Fixed
-----
- Optimize ``variant-annotation`` process to handle a larger
number of variants
- Fix the disabling of BAM writer input in ``vc-gatk4-hc``


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Added
-----
- Allow overriding docker image prefix via environment variable

Fixed
-----
- Normalize project name from `resolwe-bio` to `resolwe_bio` in about file
to ensure setup.py is compliant with PEP 625 standard


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Added
-----
- Add filtering ``Variant`` by ``VariantExperiment`` and ``VariantCall``
- Use generic permission filters when filtering variants by related models
- Return only distinct ``VariantExperiment`` objects
- Add ``--bam-output`` input argument to ``vc-gatk4-hc``
- Add ``--max-mnp-distance`` input argument to ``vc-gatk4-hc``

Changed
-------
- Change output data object name in ``gtf-to-bed`` process,
add geneset as a required field
and hide canonical transcripts table if gene feature type is selected


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Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 42.x


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Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 41.x
- Change ``reference`` and ``alternative`` field types in ``Variant`` model


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Added
-----
- Allow filtering ``Sample`` by ``Variant``
- Allow filtering variant annotations by variant id
- Add filters to ``Variant`` and ``VariantCall`` objects
- Add ``known_fusions`` file input to ``arriba`` process and
``gene-fusion-calling-arriba`` workflow

Changed
-------
- Change ``variant-annotation`` process
to skip downstream/upstream and intergenic variants
- Change clinical diagnosis and annotation fields type to text
- When filtering variants do not return duplicated objects
- Optimize resource usage in processes ``bbduk-single``, ``bbduk-paired``,
``upload-fastq-single``, ``upload-fastq-paired``,
``files-to-fastq-single`` and ``files-to-fastq-paired``
- Update the ``pca`` process with the functionality from the
deprecated ``pca-beta`` process
- Bump resources requirements for ``arriba`` process

Fixed
-----
- Change max char length of REF and ALT fields
for variant model to 150
- Fix failing requests in the ``geo-import`` process by using eutils for
fetching data from SRA
- Fix rendering of ``star_index`` input field in
``gene-fusion-calling-arriba`` workflow


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